Occasion-of-ISC2020

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ABSTRACT EXTENDED

1. AN ELEMENTARY TOPICAL EXPOSURE WITH BENZENE DIMER

A beginning can be made with the simple case of benzene-dimer. The benzene dimer seems to be
encountered in vapour state, and certain rotational constants, seems to have been amenable for
experimental measurement by microwave pulsed-nozzle FT experiments. However, it is not at all
difficult to draw two identical benzene molecules in varying relative disposition and calculate
theoretically molecular properties. Three such dispositions are described and depicted below:

Range Range
decreases decreases

FIG.1 On the Left Hand Side, 1H (proton) NMR is shown, and on the Right Hand Side, the 13C
calculated spectrum.

The benzene dimers above were generated by first drawing an optimized benzene structure and
then, copying the same, and pasting and placing at the appropriate centroid-separation distance. The
inclination of one of the structure is changed with respect to a vertical axis; and thus the three
different dispositions above were obtained. Each one of them submitted for NMR calculation
without optimizing the dimer.
In the 13C NMR, the two benzene molecules have grouped into two different ranges of Chemical
shift. For 1H NMR the pattern is so evident; Obvious changes in the range of chemical shifts of the
rings are evidenced for the two rings in case of both nuclei.
Because the dimers are themselves not optimized, the term “motives” may not be applicable. Never
the less the results are informative.
The importance of such calculations would be much more evident when non bonded aromatic rings
occur in the neighbourhood of each other due to the secondary and tertiary structures of biological
macro molecules. Typical contexts are described (1) in connection with occurrence of packing of
aromatic rings against tryptophan residues in proteins. Generating patterns of such Calculated NMR
spectra and cataloguing might be helpful in identifying relative orientations by using

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crystallographic data, generating such structures in the structure editors and submitting them for
NMR calculations. It may not be necessary to handle any such dimer structures experimentally and
obtain NMR spectra from spectrometers.
THE NMR SPECTRA for this structure of DIMER can be simulated (2) using FTNMR Simulation
software using the Chemical Shift values obtained from QM Calculations and the tabulated J
coupling values for benzene protons at VARIOUS Magnetic Field values corresponding to proton
frequency from 100MHz to 2000MHz (2 GHz). Commercial spectrometers currently available
have a maximum frequency value 1GHz. Thus the value of simulated spectra is that most of the
advantages of obtaining spectra at Higher fields would be available in frequency ranges in which

FIG.2 A dimeric structure for NMR Simulation (See Fig.3)

one cannot obtain experimental spectra for want of spectrometers at such high fields. More over the
calculated values of chemical shifts and the J values from tabulations can be used to simulate at
higher fields to obtain simplified patterns for recognition of occurrences of aromatic ring stackings /
packings. Such set of simulated spectra are depicted in FIG.3. The NMR Simulation software used
for the calculations of spectra in FIG.3 is from the link given in the webpage for nehu-saif (3). This
illustrates the perspective QM Calculation together with spectral simulation can stand alone without
the necessity to refer to experimental values.

2. A BIT MORE LEAD INTO THE TOPIC OF THE PAPER: POLYMER PMR

Having got an exposure to the theme of this contribution, a bit more lead into the implications of the
theme would be possible by considering the case of styrene polymer, where a stand- alone
theoretical result can substantiate the practically fictitious conjecture. To explain this case of
polymeric styrene further, the PMR spectrum of a polymeric styrene could be explained and
simulated convincingly by NMR spectral parameters attributable to a cyclic dimer of styrene. Thus
this cyclic dimer structure which seemingly is a much simpler chemical structure as compared to
the structure of the polymer is termed as “fictitious spin book keeping structure”. This further
sounds as a strange situation when the literature search does not have any record of this particular
dimeric isomer as a known compound but another isomer is well known.

Thus an effort could be made by optimizing a styrene isolated molecule to obtain a convincingly
stable equilibrium structure and draw two such identical molecules conveniently poised or forming
a dimer when the two molecules are subjected to Geometry optimization. If the dimer is more stable
than two identical monomers, the variation principle should lead (FIG.4.) to the more stable

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configuration for the two molecules together. In such a case what is the resulting isomeric
conformations and for that resulting stable dimer what are the chemical shift values obtained by
QM calculation and how the simulated spectrum would look in comparison to the experimental
spectrum (FIG.5.). This also would indicate a reason if anything specific exists, as to why this
compound is not known in literature. (4)

FIG.3: PMR simulation of BENZENE DIMER at several proton NMR frequencies
(Spectrometer frequencies). The simulated spectra beyond 1GHZ is currently not possible to
obtain experimentally since spectrometers are not available at these frequencies; benzene dimer
itself is such an imaginary compound that it is not possible to get sample to supply for recording
any spectra.

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FIG.4. Images of the situation corresponding to visualization of iterative sequences.
The two molecules initially placed at different distances; at a closer distance the propensity for the
formation of dimer increases. These details are illustrated elaborately at reference (4).
The dimeric structure and the corresponding calculated NMR spectrum are depicted in FIG.5.
It could be found that the required conformation does form by such dimerization and the calculated
NMR structure also resembles the experimental pattern than the other possible conformations.

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FIG.5. Dimer formed and PMR spectra calculated; different views of resulting dimer structure.
3. TOPICAL APPROACH TO INCREASE EFFICIENCY OF CHEMICAL PLANT

The next illustration would be that of handling an ensemble of water molecules (5).

FIG.6. The Solid TiO2 surface and the reactions envisaged in the polluted water medium.
The situation is when small organic dye molecules present in industrial effluents pollute the water
and by the AOP process the task is to decompose and degrade these organic pollutants. The TiO2
semi conductor material with appropriate band gap energies can be irradiated with em radiations to
produce electrons and holes. The water molecules from the bulk reach these surfaces and reacting
with holes can produce radical products by splitting water and the reacrtive radicals further react
with dye molecules at the surface and decompose them. The way QM studies can be made for this
context is to consider the radical species, and the dye molecules together and submit the
combination for QM investigation of the reaction characteristics. But the production of radical
product from water in.situ at the surface of the TiO2 and the reaction with dye molecule requires a
consideration of diffusion phenomena and which is not a simple task,

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For example the FIG.7 displays a result: That 12 water molecule ensemble is considered as a
molecular system to be subjected to Geometry Optimization. And, this system is attributed to have
4 -ve charges and submitted for GO.

FIG.7. 12 water molecules with +4e added is submitted for G.O. by PM3 semiempirical method
at ARGUSLAB computational chemistry portal. On the RHS is the situation of this system which
has gone through 60 iterative steps of GO (not yet converged).
The situation on the RHS indicates certain molecules have one or both of their bonds elongated. It
was ensured that the intermediate state when the same 12 water system is subjected to GO without
adding 4e to it, this peculiarity of bond elongation does not result for the 60 steps or even till the
end when the system attains 12 water attains energy minimized equilibrium distribution and GO
converges. During this time interval of 60 steps, the evoloution would involve a diffusion process in
water which would be rearranging the molecules. Thus at intermittent iterative steps it is necessary
to stop the calculation process, edit manually based on chemical intuition and continue the iterative
optimization from that stage onwards. These kind of manoeuvres seem to yield some insights as to
how exactly to regulate the radical productions and reduce the radical recombination processes to
increase the efficiency of AOP. These results can be appropriately translated into experimental
conditions while designing water purification plants. These details as the chemists would require to
know have been pointed out in reference (5).
FIG. 8. Is a situation that depicts a kind of end result as purportedly what happens in the
experiments. Such studies are mostly are theoretical investigations of experimental phenomena, but
till the end no comparison with experiment is required and sometimes the results when they are not
the same as what experimentally thought off, then calls for additional theoretical studies, finally to
be leading to novel experiments.

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FIG.8. An end convergent result, similar to experimentally envisaged production of radicals,
and H2 evolutions stoichio metrically accounted. From ref (5).

4. FOR THE INTEREST IN CHEMISTRY FROM OUT OF THE LAB
INFORMATION

The next system to consider from the stand point of the theme of this paper is the combined
molecular system of Methane and Benzene. This combined system (one gaseous and the other
liquid in room temp) though experimentally not encountered in Chemical laboratories as any
requirement for such a system, can be studied by QM abinitio methods. To consider in an
elementary way, the Benzene has D6h point group symmetry and there could be 6 bond dipole
moments but net molecular dipole moment is zero. Similarly the Methane molecule ahs a Td
symmetry and could have 4 bond dipoles and no net Molecular dipole moment. These molecular
dipole moment situations of the two highly symmetric molecules are borne out by QM methods.
However, when the two molecules with their individually optimized molecular geometry are drawn
together at a distance of separation of about 5 Angstroms there is a non vanishing net dipole
moment generated for the combined system and according to the calculation engine such a Dipole
Moment is indicated to be located somewhere in the common region for the two molecular system.
No GO is carried out only simply single point energy calculation which also calculates the net
dipole moment. This raises the question as to
how Charge movement occurs to cause a net transfer of charge from one of the molecule to the
other there can be net equal and opposite charge separation and a well defined dipole moment. A
calculation of NMR spectrum, particularly PMR chemical shifts, results in a varied PMR pattern
than the simple two line (one

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benzene line at aromatic protons vale intensity 6 & one methane proton line at methane chemical
shift value with intensity 4) for the non interacting systems. This study gets an elaborate treatment
with more involved consideration. Obviously a Benzene+Methane system is not of much relevance
to chemical study.

FIG 9. A typical example of the combined Methane & Benzene study, indicating net dipole
moment, variation of proton NMR pattern indicating atomic charge variation merely at a farther
distance compared to bond lengths.

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RFERENCES:

(1) Uttamkumar Samanta, Debnath Pal and Pinak Chakrabarti, (1999), Packing of Aromatic Rings
Against Tryptophan Residues in Proteins, Acta Crystallographica, Section D, D55, 1421-1427.

(2) S. Aravamudhan, (2016) personal web domain; http://www.ugc-inno-nehu.com/ This

benzene dimer structure calculated NMR data at: http://ugc-inno-nehu.com/Benz2-

Benz1/archive159831.tar this link archive can be imported into the www.webmo.net

computational chemistry portal and results can be viewed.

(3) S. Aravamudhan, (2014), personal web documentation –internet resource. http://ugc-

inno-nehu.com/saif_nehu.html at this webpage almost at the top find a hotlink Jump

to FTNMR SIMULATOR.

Clicking on this link would let the page display jump to a link again:

File HERE Download to Install FTNMR Simulator from which an Fidwin.exe

simulator file can be downloaded to install the simulation software in the computer.

Take proper care at the instance of downloading and installing.

(4) S.Aravamudhan, (2018), Plenary lecture, Visualizing a Cycloaddition by the Abinitio SCF

Methods for the formation of Polystyrene, http://www.ugc-inno-nehu.com/events-

2018.html#bhc

(5) S. Aravamudhan, 2017, Studies by Computational Chemistry on the Removal of Water
Pollutants using TiO2 /O2/H2O2 Photo catalytic AOP Activity, Personal Webpage, Internet
Resource, http://www.ugc-inno-nehu.com/events-2017.html#E09

(6) S. Arvamudhan, 2018, personal web domain content, Internet resource; Image files
http://www.ugc-inno-nehu.com/ISC105-OSU/image-files/

FURTHER SUGGESTED READING:
http://ugc-inno-nehu.com/compile/07-2013-ICETCS-CUG-sa.pdf
http://ugc-inno-nehu.com/JMSE-A5-2015-p181-SA.pdf
http://ugc-inno-nehu.com/IJRDET-AugVol4Numb8-paper-sa.doc